Move ontology

[samwaseda]

In the ongoing efforts to define the interface between semantikon and workflow managers here, I started moving the knowledge graph part to semantikon.

[github-actions]

👈 Launch a binder notebook on branch pyiron/semantikon/move_ontology

[samwaseda]

@liamhuber How do I run integration tests?

[liamhuber]

@liamhuber How do I run integration tests?

I'm not sure what you mean -- they're already running.

Tests are all in ./tests. The full OS and python version matrix only runs on ./tests/unit, but the "Tests-and-Coverage" runs on a different folder. The default is just ./tests, so the integration and benchmark jobs get hit here too (you can scroll up in the last link to look at the default value, and see in this repo that we don't override it.)

Your local change here even forced the integration test to cause the "Tests-and-Coverage" job to fail, so I think you're A-OK?

[liamhuber]

It's not like pyiron_base or whatever where you need to explicitly add a tag to run them -- they always run, but the compromise we make is that they only run on a single OS-python version pair.

[samwaseda]

Oh ok it's part of Test-and-Coverage. I didn't know that. Is there a possibility to use a different yml file for the dependencies?

[liamhuber]

Mmm, not really, no. There is a variable to change it https://github.com/pyiron/actions/blob/55c8edbda302d784541ee7777d62f2b90552283c/.github/workflows/push-pull.yml#L84, but this is for all the tests in tests. I'm not 100% closed to changing that, but I lean against it. IMO everything in ./tests/ should run on the same env.

There are separate variables for the docs and notebooks tests though. Since this is an integration test, it sounds like some sort of bigger end-to-end thing...would it fit well in the notebooks? This would get it as part of the CI, make sense for a bigger-scoped integration-like thing, and give you a sensible reason to modify the environment.

Without more details on what test you're thinking of running, I can't give more specific advice.

[samwaseda]

So the idea is to move the whole thing from pyiron_ontology to semantikon, but if I understand the current plan correctly, we don't want semantikon to depend on pyiron_workflow. But I wanted the integration tests to test the semantikon - pyiron_workflow interactions.

[liamhuber]

Ah. Yeah, in the long run I guess I'd rather have those tests in the pyiron_workflow repo, but I like your action plan. That definitely sounds like something that is appropriate for the notebooks, as it's a good demo of "and here is the type of cool thing you can do with semantikon". So, I'd really not just have the test but annotate the notebook nicely enough that it really does serve the dual purpose of testing and education.

[codacy-production]

Coverage summary from Codacy

See diff coverage on Codacy

Coverage variation	Diff coverage
✅ -0.47% (target: -1.00%)	✅ 95.10%

Coverage variation details

	Coverable lines	Covered lines	Coverage
Common ancestor commit (eead0cc)	145	139	95.86%
Head commit (b07afb9)	282 (+137)	269 (+130)	95.39% (-0.47%)

Coverage variation is the difference between the coverage for the head and common ancestor commits of the pull request branch: <coverage of head commit> - <coverage of common ancestor commit>

Diff coverage details

	Coverable lines	Covered lines	Diff coverage
Pull request (#50)	143	136	95.10%

Diff coverage is the percentage of lines that are covered by tests out of the coverable lines that the pull request added or modified: <covered lines added or modified>/<coverable lines added or modified> * 100%

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[coveralls]

Pull Request Test Coverage Report for Build 13249172463

Warning: This coverage report may be inaccurate.

This pull request's base commit is no longer the HEAD commit of its target branch. This means it includes changes from outside the original pull request, including, potentially, unrelated coverage changes.

• For more information on this, see Tracking coverage changes with pull request builds.
• To avoid this issue with future PRs, see these Recommended CI Configurations.
• For a quick fix, rebase this PR at GitHub. Your next report should be accurate.

Details

• 0 of 0 changed or added relevant lines in 0 files are covered.
• No unchanged relevant lines lost coverage.
• Overall coverage decreased (-14.5%) to 81.206%

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Totals
Change from base Build 13230530735:	-14.5%
Covered Lines:	229
Relevant Lines:	282

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💛 - Coveralls